The Secret Agent Conundrum
by kbcountry37
Summary: When Shamy turns evil, the rest of the gang turn into spies to stop them from destroying the world. However, when their next target is Raj, what do they do? WARNING: Mild language and sexual content!
1. Chapter 1: The Mission

**Hi everyone! Welcome a story that's been biting at the inside of my brain for about a week now...thanks to SlightlyOffKey. You really have gotten me to think about this and that's really awesome that an idea came from a tweet! **

**Remember, that I do not own The Big Bang Theory. I am merely using the names and likenesses of these amazing characters. They are owned by Chuck Lorre, Bill Prady, CBS, and Warner Bros. If you have any issues with these characters, it's their fault not mine. **

**Reviews/alerts are good and appreciated. They will definitely make me want to update sooner. I will try to respond to each. I do work, so if this story goes for a few days without an update, that is why, but I will finish this fic because it has nibbled at me, and it needs to be seen by this world. Ok...enough with this! Here is The Secret Agent Conundrum!**

The Secret Agent Conundrum

Chapter 1 – The Mission

Rajesh Koothrappali sits in his lair wearing his fanciest pajamas and drinking the best brandy he's ever tasted. He's checking things out on the interwebs. Just your typical things, you know the news (he has to know what is going in the world), his pseudonym Facebook and Twitter accounts (why in the world would he use his real name-and he doesn't use them much-but for once he's had a quiet night and decided to check them out), and his email (which he sees that there is an email marked urgent from Leonard. He opens it up and reads this:

_Dear Raj,_

_It has come to my attention that your sister, Priya, is working for the evil Dr. Cooper and his girlfriend, Dr. Fowler. If my intelligence is correct, you are her target. What I want you to do is to get to her before she gets to you. _

_You know that if you are caught, you could end up tortured to death. Oh, what the hell, we all know what Sheldon is capable of and with Amy's neurobiology background, there are ways they can cause you to be tortured beyond anything you'd ever want imagine._

_Let me know ASAP when you get this message if you accept or not. _

_Thanks,_

_Leonard_

_PS – If you take this, and you know this, you are greatly putting your life on the line. I know you and Priya are related, but you need to realize that she doesn't care that you are her brother or a crash test dummy. And if any help is needed, we will all be there at a moment's notice. It's what friends do._

Raj sat back from the screen and took a sip of his brandy. "Why would Leonard ask me to put my life on the line like this? And why Priya? Oh, Sheldon, you rat bastard. You are messing with forces beyond anything you've ever imagined. Even if I have to put Priya in jail, I will stop Sheldon and Amy."

Raj hits the reply button and types this:

_Dear Leonard, _

_I will accept this mission with pride. I was scared at first, but I realize that Sheldon and Amy need to be stopped. They've messed with the wrong guy. _

_Also, your offer for help. I beg of it. I am afraid I will not be able to do this mission alone. This is the largest one I've had and I don't want to get caught. I don't want any of us to be caught. I know you know where I'm going with this, so I will stop myself._

_Thanks for all the help,_

_Raj_

Penny is sitting at Leonard's desk when she sees Raj's reply came in. "Leonard, Raj has replied!," she yells.

"Shhhhh! Penny, people can hear us! We don't want that!," he responds. "What's it say?"

Penny reads it to Leonard. He walks over and says, "Penny, I need to reply to this immediately."

"Let him know that I'm all in for helping as well. I need to call Bernadette and Howard. I have a feeling we are going to need to the whole team.," Penny says.

"Yes, most definitely. I will respond with what we have so far."

_Dear Raj,_

_Penny and I are on board for helping you out on this mission and will be over there first thing in the morning to begin plans. I'm sure you are safe tonight. No one but us four know where you are._

_Penny is calling Bernadette and Howard now. We will let you know if they agree when we get that information. _

_You know how Bernie is these days, she doesn't want anything to happen to Howard. I think for this mission he will reside at your lair and run our computer diagnostics and hack into things that we need hacking into. That should ease her mind._

_Thanks,_

_Leonard_

Raj reads this and smiles. He thinks, "I'm glad I have such awesome friends."

Just then, two emails appear in his inbox. One of them is from Leonard, the other from Howard. Raj opens up Howard's email first.

_Dear Raj,_

_Just got the call from Penny. As always, Bernie and I will be pleased to lend our services to stop Sheldon and Amy. _

_As Leonard has probably already told you, I am going to be staying at your lair while you guys are on the mission and helping in any way possible with tech support, and I mean any way._

_We will be over first thing in the morning with Leonard and Penny to make the plan. Don't worry buddy, we've got this. Priya and eventually Sheldon and Amy will be stopped. This is my promise._

_Oh, and Bernie says she's bringing breakfast. _

_Thanks,_

_Howard_

Then Raj opens up Leonard's email. It was short and sweet.

_Dear Raj,_

_Howard and Bernadette have accepted. We will all be there at sunrise, and Bernie's making breakfast Howard says._

_Thanks,_

_Leonard_

Raj sends both Leonard and Howard the same email:

_Hi guys,_

_Thanks so much for helping out! I'm so very grateful! You have no idea! _

_See you all tomorrow!_

_Leonard – By sunrise, you mean when we first see any glimpse of light, right? I'll be up expecting you around 6 am._

_Howard - Tell Bernie thanks, I love her pancakes. Yum!_

_Thanks,_

_Raj_

Raj finishes and shuts down the computer. He doesn't need it for the rest of the night.

He walks into his bedroom and turns on the lamp on his night table. He walks over and shuts his door. He sees someone who he knows all too well standing behind it waiting for him.

"Priya!," he screams.

**Hope you liked it! I would leave you with suspense, wouldn't I? What is Raj going to do? What's going to happen to him? How did Priya find him? It will all be answered! Reviews/alerts are awesome! So, thanks in advance!**

**Remember it's an AU world, in which these characters have turned into spies; you will just have to read to find out more...I hate spoilers and never read them, so I will give you the same courtesy here. These characters that we all know and love are going to be OOC. Especially Raj...who's selective mutism has been removed for me to more easily write this concoction of a story. I know it doesn't seem like it now, but I wanted to forewarn you! THAT IS ALL!**


	2. Chapter 2: The Hostage

**So, chapter 2...what can I say? Other than I am sorry for the cliffhanger. Yeah, I hate them too, but what's done is done, right?**

**Thanks for the great reviews/alerts...the more I get, the more I write and faster too.**

**The typical disclaimer states that I do not own anything that you recognize from TBBT and that these wonderful characters are the creation of Chuck Lorre and Bill Prady. Blame them if you have an issue with a character not me.**

**With that being said, enjoy!**

The Secret Agent Conundrum  
>Chapter 2 - The Hostage<p>

Again, Raj looks at the woman standing in front of him in shock. He knows her all too well. He spent most of his childhood hiding from her, just to avoid her physical assaults.

"Priya?," he yelled again.

"That's right, Rajesh. It's your little sister, Priya. I've come on strict orders from Dr. Cooper.," she said in an evil tone.

"Yeah, I know that, but I have one question to ask you. Why am I the target? Why not Wolowitz or Leonard? Penny or Bernadette? Why am I the first target? And how in the world did you find me? This location is top secret!"

"That is for me to know and for you to find out. And Rajesh, it can't be that top secret if I found it, now can it?"

"But...but...oh, Sheldon! He's such a rat bastard! UGH! Seriously, how did he convince you to go against me?"

"Again, for me to know and for you to find out."

"But...But..But.," he stutters.

Raj makes a run for it. He runs through the main room and out the front door into the fenced in yard. As he is running he hears Priya yell "राजेश, गेट बेक हियर हे यू सों ऑफ़ अ बीतच!" ("Rajesh, come back here you son of a bitch!") in Hindi. He realizes that he hasn't heard that phrase yelled at him in that language since before he left India and that it was his mother who had said it. 

He then realizes that he is not strong enough to pull himself up and over the fence and sees his sister running right at him. Raj reaches in his pocket and feels his panic alarm. He presses the button and hopes for his friends to help him.

"After all, that was the whole point of that device anyway.," he thinks.

He backs up against the fence and braces for the worst to come.

**MEANWHILE AT HEADQUARTERS...**

Leonard and Penny went to bed after they received Raj's last email. When they hear a screeching noise going off they both knew that the panic button had been pressed. They also knew it had to be Raj.

Leonard's cell rings on the night table. It was Howard.

"Hi, Leonard. Do you have an alert?," he says.

"Yes, it woke both of us up. Why?," Leonard responds.

"The alert came from Raj. He's in his yard. I'm only assuming trapped by something or someone."

"Yeah, I know who that someone is! Thanks Howard. You and Bernie meet us there. Penny will send you the plan from the road."

"Got it!"

Leonard hung up and jumped out of bed. Penny followed him. She didn't have to second guess what that conversation was about and why Raj had pushed his panic button. They get dressed in a hurry and grabbed their equipment. They ran out to their car they only used for missions and hurried to Raj's lair.

**BACK AT RAJ'S...**

Priya attacks Raj and brings him to the ground. She kicks him in the groin.

Raj's eyes fill up with tears. Priya has kicked him here before, but never this hard. This hurt. "If I get out of this alive I'm gonna need some ice.," he thinks. He rolls around on the ground . The only sound he can make is a loud grunt.

Priya grabs his hands and ties them behind his back with the rope she had in her backpack. Priya grabs her phone and calls our evil genius Dr. Cooper to inform him that she has success. He sends for transport of Raj back to his place for interrogation/torture from Dr. Fowler.

When she gets off the phone she smiles really big and thinks, "I've got you now, Rajesh. I've got you now!" Just then, she hears footsteps behind her. She turns around and sees Penny and Bernie standing there with their arms folded.

"Wha...What? You guys? How in the world did you know I was here?," Priya yells.

Penny laughs. "Priya, Priya, Priya. Hmmm...Hmmm...Hmmm. What kind of friends would we be to Raj if we didn't respond when he sends out a distress signal? Huh?," she added.

"How did you get here so fast?, " Priya yells.

"That is for us to know and for you to never find out.," Bernadette states.

"That's right, it's top secret information, Priya.," Raj grunts from the ground.

"It will come out in the end. Dr. Cooper has a plan for all of you, and in the end all five of you will be vegetables laying in some hospital somewhere or worse Dr. Fowler could decide to send you to your graves. It really all depends on how Dr. Cooper feels that day. My advice don't make him mad.," Priya said.

"I know what Sheldon is capable of, Priya. I've known him a long time. I actually never expected this, but Leonard always assumed it would.," Penny stated.

"Oh, quit with the jibber jabber, ladies and cuff her! For my sanity!," Raj grunted.

"Oh, right sorry Raj!," squeaked Bernie.

Penny grabs Priya from behind and holds on to her with all the strength in her body. Bernadette cuffs her and says, "Now you've been caught!"

Bernie leaves Priya in Penny's grip and walks over to Raj. She helps him up off the ground. She asks, "Are you OK?"

"No, but thanks for asking.," Raj grunts. "I'm definitely gonna need some ice on my groin."

Bernie laughs and lets Raj lean on her for support. She says to the handcuffed Priya in Penny's strong grip, "You don't help out Sheldon and get away with it!"

Bernadette and Raj slowly make it back to the house. Penny closely following with Priya in her unrelenting grasp.

Bernadette helps Raj to his bedroom. Leonard walks in and see that Raj is in pain. "Something I can do to help?"

"Yes. Get me some ice for my groin!," Raj grunts. "I wish I had been wearing my cup."

"Been there done that. I know what that feels like...isn't pleasant.," Leonard tells Bernadette.

"ICE!", Raj yells.

"Oh, yes. I will be right back.," Leonard says. He goes off to get Raj the ice pack he is begging for.

Penny meanwhile is forcing Priya into a makeshift cell that Howard assembled in Raj's front room. She gets her in and shuts the door. Howard locks it and stands guard. "How's Raj?," he asked.

"He's been kicked in groin and is moaning and grunting about wanting ice.," Penny replies. "I'm going to go check on him. I'll send Bernie your way."

Howard nods his head showing that he understands.

Penny walks back to Raj's room to see Leonard handing him the ice. She smiles. "I'm glad that you have your ice pack, Raj. We need to figure out how she found him and where in the world Sheldon and Amy are."

Leonard nods in agreement.

Bernadette does the thumbs up sign.

"Oh, Bernie, go help Howard guard Priya will you? If she gets out of hand, you know what to do.," Penny says.

Bernadette nods and heads to the front room to be with Howard.

**Well, that's all I can get out of this chapter. If I'm having trouble getting anything else to happen. That's usually my cue that the chapter is over. I know I am leaving you with lots of questions. I will try to answer them all inside this fic eventually. However if you want answers now, PM me or tweet me! My Twitter name is kbcountry37. I promise I respond to my tweets! **

**Also, review/add this story to your alerts. The more I get, the faster I update and the more I write. Plot suggestions will be taken into account and I will try to work them in if I can. Thanks to all the people who have reviewed so far. **

**I realize that Raj seems whiny in this chapter, but remember he's in pain. I'm not a guy, but I've seen plenty in this state and can guess as to how it feels. I never want to cause a beloved character misery or pain, but in this case it seemed necessary. **

**REVIEWS ARE GOOD! TWEETS ARE GOOD! **


	3. Chapter 3: The Reason It Happened

**Hello everyone! Sorry this took SO LONG! Life gets in the way, and boy did mine get in the way, let me tell you. I love writing, but apparently people in my family don't seem to give me time to do so. I finally got around to getting some alone time and this is what became of it! Enjoy chapter 3 of The Secret Agent Conundrum!**

**PS – Prady and Lorre own it all...I own nothing!**

**WARNING: This chapter is a flash back and it does contain some moments that may be too mature for younger eyes.**

The Secret Agent Conundrum - Chapter 3: The Reason It Happened

Sheldon sits in Amy's lab waiting for her to finish her day so they can go on their planned date night. As Amy is working she realizes she made an awful mistake with one of her experiments.

"Oh no, oh no, oh no!", Amy cries from the adjoining room to her lab.

Sheldon hears hear cry from the other room and unthinkingly runs to see what is wrong with his girlfriend. "Amy, are you ok?"

"Sheldon, you don't need to be in here. I've made a horrible mistake with an experiment." She begins to sob. "I think that is has turned into something radioactive.", Sheldon could hear her say through her now steady sobs.

"Radioactive! I'm getting out of here!", he yells.

"It's too late, Sheldon, you've been exposed, as have I."

"Oh, God, why have you forsaken me, even though I doubt your existence?", Sheldon cries out.

Amy wonders what has come upon her and her boyfriend. "_What have I done?"_, she thought. Her tears now quieting, but you can clearly see the worry on her face. Amy walks over and closes the door to the room. "We need to stay in here. This radioactivity can't be spread all over Pasadena."

"What about our date?", he asks.

"Our date will be spent in a radioactive lab, Sheldon."

"WHAT? NO! I can't believe this!"

"Sheldon, do you really want to go to The Cheesecake Factory and infect everyone in there, including your neighbor and my bestie? Because if Penny gets infected then Leonard will, unless you get to him first, which is a high possibility since you live with him. However, I don't want that happening.", she told him. _"What am I going to do to decontaminate us? How will this affect us from now on?"_, she thought.

"That's a fair argument. I do not want Leonard and Penny to be contaminated, no matter how mundane and workaday they are."

"Come on, Sheldon. We need to decontaminate ourselves."

"Where? What? How?"

"In the decontamination unit through that door.", she said, "For a genius, you really are not thinking like one."

"HOW DARE YOU SAY THAT, AMY?"

"Well, it's true!"

"_I hate to admit it, but she's right. I'm not telling her that though."_, he thought. "Ok, how do we proceed?", he asks her.

"Come on." She grabbed his arm, although he was quite reluctant of her touch at first , and she led him through the door to the decontamination chamber. "Take off your clothing."

"WHAT?"

"Take off your clothing, Sheldon. They are contaminated and we need to dispose of them to decontaminate.", she replied.

"NO, NO, NO! We are not getting naked together!"

"Sheldon! We have to! It's the only way to decontaminate! Do you not get that?"

"I do not have a change of clothing, I can't dispose of them!"

"It sounds like you would agree to the decontamination shower?", she asked. He nodded his head yes and sighed. "What's the sigh for, Sheldon? Are you scared of what you might find out?", Amy said slighly.

"Um...um. It sounds to me as you are going to take this opportunity to try to have coitus with me and get decontaminated too. I don't like it! I don't like it at all!", he said.

"Ok, but we need to get decontaminated. What do you suggest?"

"I suggest we take our decontamination showers separately."

"I'm afraid that we can't do that, Sheldon. There are only enough decontamination agents for one shower and they highly recommend that these showers are not taken alone."

"WHAT? One shower? Oh, I'm so screwed!"

"Not if we shower together.", Amy said snarkily.

"Oh, ok. I see where your reasoning is and this is an emergency.", he said.

Sheldon and Amy begin to strip their contaminated clothing and put them in a bag that prevents anything else from being contaminated. All that they had left were their undergarments and Amy really thought those should be removed too.

"I think we should remove our undergarments too. We need full decontamination.", Amy said.

"NO! You've already got me into my underwear, what more could you want?"

"SHELDON! You know where I'm coming from here! This is not a time to dilly dally around. Do you want to walk in the outside world again or do you want to be trapped in this room forever?"

"Yes, I do. I just think that taking off our undergarments is going too far. My mother once said, 'Never let a girl see it unless you intend on spending the rest of your life with her.'" _"Wow, I guess Mom wins."_, he thought. He reaches for his underwear and drops them, revealing it all to Amy.

"Oh, my!", laughs Amy.

"What?"

"Nothing, nothing at all." Amy turns her head so she doesn't feel her sexual attraction to Sheldon. She knows that it will be hard to not show it, but then she thinks, _"Oh. Come on! I'm his girlfriend! I'm supposed to sexually attracted to him!" _She unsnaps her bra that hooks in the front and drops it in the bag with her other clothing. She hesitates for a moment and then drops her underwear and tosses them in the bag with the bra. She hesitantly turns around and lets her boyfriend see her naked for the first time.

"Um...um...um.", stuttered Sheldon.

"What's wrong Dr. C? Cat got your tongue?"

Sheldon is speechless and walks straight by Amy and to the decontamination shower.

Amy ponders what just happened and walks over to shower only to find a very different Sheldon.

**A/N: YAY for Shamy! I had a few reviews ask me to reveal how they turned evil. Well, these next few chapters are just that, how they turned evil in a flash back! You'll see where I'm getting at, don't worry! And I fought and fought with Shelly all day to write this. It's been quite hard because I am quite adamant against Shamysex, however I reminded myself something, this is an AU fic and anything goes! I still can't believe I got them that close to it though. Oh, well. We will see what happens and them turning evil in the next few chapters. We will eventually get back to Raj and the gang! PROMISE! This has to be shown or it won't make sense!**

**PS – REVIEW PLEASE! I like reviews! I will try to update more often, but life gets in the way. So sad really that it's the truth. However, I will eventually finish this fic, I promise!**


	4. Chapter 4: The Reason It Happened: 2

**The Secret Agent Conundrum – Chapter 4**

**The Reason It Happened: Part 2**

**A/N: Hello all! Hope everyone is OK! I know it has been over two months without an update, but can I say life got in the way again? It truly is the case. Now, that I've quit the job that took all the life out of me...at least that's what it felt like...I can try to refocus on getting this and The Double Minion Catalyst completed. :)**

**Lorre and Prady own it all! I own not a thing, not a dang thing!**

* * *

><p>Amy walked into the containment shower to see Sheldon sitting on the floor with his knees up to his chest, his arms hanging over them, and his head being supported by them. She thought she could hear the faint sounds of crying through the water running from the shower head. "Sheldon, are you OK?" she said with a slightly fearful tone in her voice.<p>

"OK! OK! Am I OK? Amy, no I'm not OK!" Sheldon yells through the down pour of water showering over him.

Amy stands there confused at Sheldon's reaction and step in the water and feels a large amount of emotion fall upon her. She slides down the wall and sits next to Sheldon, now realizing what is happening to both of them. She reaches up and turns the water off for both shower heads. She stands up and grabs Sheldon's arms and tries to pull him off the floor and into a standing position. Amy uses all her strength, which she admits isn't much, to pull her boyfriend from the floor. She finally accomplishes her mission and walks out of the shower realizing that whatever has happened can't be good.

She walks back into the stall and hands Sheldon a towel, which he takes gratefully and begins to dry himself off. Amy starts drying herself off as well and looks at Sheldon, only to notice the change that has happened. "Sheldon, something is wrong! Something is very wrong! Something reacted with the water in the containment shower with something that we had on us. It has changed our brain chemistry and I can prove it!" she yells. "What did you feel when you touched the water?"

Sheldon looked at Amy and said, "A huge rush of emotion, something that I've been trying very hard to hide. There is a reason, Amy dear, that I did that! Not anymore! I have plans! I don't need proof that our brain chemistry has changed. I know it has!"

"Sheldon, don't you want to know what caused it? I can figure it out so we can reverse it! We are turning into evil geniuses! This isn't good. I'm not an evil person!" Amy yelled back.

"I don't care, Amy! I have been holding back all these emotions for so long! Now, I will unleash my fury on the world and take revenge on every bad thing anyone has ever done to me! You are my only exception, Amy! I love you and don't want any more harm to come to you!" he yelled.

"Then we need to figure out what happened so we can go back to our old selves!" she replied.

"NO! NO! NO! For too long, I have sat and let people bully me and laugh at me. Make jokes about me and point at me. Don't think I didn't know. My amazing hearing has always been quite an amazing thing. Well, now it's payback time! Amy, I know you feel the same way. What about those girls in high school that put the Rogaine in your lotion? Wouldn't you love to get revenge on that?"

"Yes, but..."

Sheldon interrupted, "OK, then. Shall we get something started?"

Amy couldn't help but cave to Sheldon's wishes. She knew with all her heart that she was right. Even the woman she called her Bestie had said some stuff that she did not take too well. She held it in because that's what she did. That's how she was. Not anymore. Now it's Amy and Sheldon against the world and she loved...no adored the sound of that.

* * *

><p>Leonard and Penny were sitting in 4A cuddling on the couch, leaving the cushion on the far left free. They knew that if Sheldon were to come home from visiting Amy's lab and saw them in his spot all hell would break loose. They were pretty much right about the hell part.<p>

The door opened to the apartment to find very angry versions of Sheldon and Amy rushing through the door.

"What's wrong Sheldon?" Leonard asked.

"You are what's wrong! And you! Oh, don't think you are gonna get off the hook here, Penny! Just wait! Wait to see what you have done! I will get my revenge upon the world!" Sheldon yelled and he walked to his bedroom to grab his belongings so he can move out and into somewhere more secret for his and Amy's operation.

Amy followed behind him with the same energy that Sheldon left room in.

Penny stood up to follow when she felt Leonard pull her back down onto the couch to prevent her from doing so.

"Penny, something happened in that lab today. I'm a scientist too and I know when something bad has happened. Something bad has happened to Sheldon and Amy." Leonard said.

"Ok, how do we figure out what happened? They aren't going to tell us!" Penny replied.

"We are going to have to do some detective work and figure it out ourselves." He replied.

"Leonard, I'm not a scientist. I don't know anything about biology or physics. What do you suggest I do?" she asked.

"You can be in charge of the command center. You know how to do all that kind of stuff." he said.

Just then Sheldon and Amy walked back into the living room and they left with a few final words from Sheldon, "Beware of your every move! It might just be your last one!" They both walked out of that door only to be heard from if something went horribly wrong.

"Um, remember when I said that Sheldon was one lab accident away from a super villain?" Leonard asked Penny.

"Yeah." she replied.

"I can't believe that I actually may have seen the future." he said in shock.

"We need to call the others and we all need to find a safe place to go so Sheldon and Amy can't find us." Penny said.

Leonard nodded and grabbed his phone and started making plans and calls to figure out how to proceed with their plan.

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><p><strong>Well, that's all for this chapter. The next chapter is still flashback mode. We are going to see what Leonard, Penny, Raj, Howard, and Bernie are planning and see how it applies to the present time line.<strong>

**I hope to update faster, again I make no promises. **

**Please read and review. I love reading your reviews! :)**


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